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Genomics

Life Science Technologies

ProteomicsóMarch 1

Fluorescence MultiplexingóApril 12

Proteomics: Maldi ImagingóMay 31

Upcoming Features

Although most microarray applications are currently research-

use-only, this technology appears poised to move to the clinic for

genomics-based applications. In fact, some products can already be

used in medical diagnostics and many more are in development.

For example, microarrays can be customized to detect small,

specific genetic changes that indicate a particular disease. In the

future, this technology will likely remain a useful tool for both

research and clinical applications

See full story on page 858.

The Clinical Aspirationsof Microarrays

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858

ProteomicsóMarch 1

Fluorescence MultiplexingóApril 12

Proteomics: Maldi ImagingóMay 31

Upcoming Features

The Clinical Aspirations of Microarrays

Although most microarray applications are currently research-

use-only, this technology appears poised to move to the clinic for

genomics-based applications. In fact, some products can already be

used in medical diagnostics and many more are in development.

For example, microarrays can be customized to detect small,

specific genetic changes that indicate a particular disease. In the

future, this technology will likely remain a useful tool for both

research and clinical applications. By Mike May

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In todayís translational genomics re-

search, says Seth Crosby, alliance

director of the Genome Technol-

ogy Access Center at Washington

University School of Medicine in

St. Louis, ìThe biggest challenge is in-

terpretation.î Available technology makes

it easy enough to collect information

from someoneís genome. The tricky part

comes in interpreting the clinical rel-

evance of that information. ìThen, one

can say a variation in a particular gene is

known to have such and such impact on

the patientís health or treatment options,î

Crosby explains.

As an example, Crosby describes a clini-

cally certified next generation sequencing

panel of 45 oncology genes offered by Ge-

nomics and Pathology Services, Washing-

ton Universityís clinical genomics labora-

tory. This panel is actively being used to

profile tumors and guide the treatment of

cancer patients. ìWe had to look at hun-

dreds of papers,î Crosby says, ìto build

a clinical-grade database of authoritative

interpretations for each clinically relevant

mutation found in these genes.î He adds,

ìThat took hundreds of Ph.D. and M.D.

hours, reading through papers to identify

the pertinent information.î

Crosby notes that, over time,

clinicians might come to understand

which changes in the genome impact a

patientís health and which are harmless.

ìOnce the lists of relevant and irrelevant

genes are narrowed down, and we

have a sense of which polymorphisms

are important, these could be used to

create a very cheap array that would help detect diseases,î he says.

Beyond being economical, microarrays also deliver manageable

amounts of data. As Crosby explains, ìMuch of the genome is

invariant.î So with microarrays, he says, ìWe collect only the data

we need.î

Developing Diagnostics

In some cases, clinicians can link specific chromosomal defects with

particular diseases, and microarrays bring new capabilities to this

karyotyping, or counting and assessing the appearance of chromo-

somes. Down syndrome is one of the best-known examples, in which

the person has an extra copy of chromosome 21. Although additions

or deletions of entire chromosomes, and even defects in parts of them,

can be seen under a microscope, microarrays reveal fine-detail changes

in chromosomes. ìUsing microarrays as tools in cytogenetics is really

accelerating,î says Andy Last, executive vice president of the genetic

analysis business unit at Affymetrix in Santa Clara, California. When

experts are asked in which areas microarrays are being used the most,

many mention copy-number variationóthe addition or deletion of spe-

cific regions of DNA, particularly those with clinical consequences.

ìThere are literally hundreds of syndromes [that have] chromosomal

rearrangements associated with a particular phenotype,î says James

Clough, vice president, clinical and genomic solutions at Oxford

Gene Technology (Oxfordshire, United Kingdom). ìDepending on

the population being tested, traditional karyotyping under a microscope

provides a diagnosis about 5ñ8 percent of the time, and a microarray

provides an 18ñ25 percent diagnostic yield. The resolution is far higher

with an array.î Still, he adds, ìThe challenge is determining if a small

aberration is pathogenic or nonpathogenic, or a variance of unknown

significance.î

ìUsing microarrays

as tools in

cytogenetics

is really

accelerating.î

Genomics

Life Science Technologies Produced by the Science��������������������� �����

www.sciencemag.org/products

To help researchers make such distinctions, Oxford Gene Technol-

ogy supplies a range of microarrays, such as the CytoSure ISCA Arrays,

which look for genetic defects involved with known syndromes, such as

Prader Willi and Williams-Beuren syndromes.

PerkinElmer (Waltham, Massachusetts) has also developed assays

for detecting disease-related structural changes in chromosomes. For

example, the company provides genomic testing of oncology samples

with its OncoChip. ìThis is a high-density whole-genome array, tar-

geting more than 1,800 cancer genes and clinically relevant balanced

translocations,î says Christopher Williams, market segment leader at

PerkinElmer. The array can reveal copy-number variations as low as 10

kilobases in the targeted regions.

Additionally, the CytoScan HD Cytogenetics Solution, from Affyme-

trix, offers probes for both copy-number variation and single nucleo-

tide polymorphisms (SNP). The probes for copy-number variation can

reveal chromosomal changes that could cause clinical concerns, and

the SNP probes help researchers assess more detail on the exact varia-

tionóspecifically the changes in individual nucleotides. ìThis is the

highest density microarray on the market,î says Last. ìItís being used in

the classical sense of cytogenetics, [to detect] inherited disorders, and

increasingly in oncology, especially [for] hematological malignancies.î

The array can reveal copy-number variations in chromosomal segments

as small as 25,000 nucleotides. For the moment, this is a research-use-

only tool, but Affymetrix is running clinical trials to test the use of this

platform as an in vitro diagnostic.

Agilent (Santa Clara, California) also makes microarrays that de-

tect copy-number variations, such as its CGH (comparative genomic

hybridization) plus SNP microarrays. ìThese can be customized from

more than 28 million probes in our library, and users can even upload

their own probe sequences,î says Patricia Barco, product manager for

cytogenetics at Agilent. Within an exon, for example, these microarrays

can detect copy-number variations in DNA segments as small as 100

base pairs. ìThese can be used in prenatal and postnatal research and

cancer,î Barco says. The most popular format, according to Anniek De

Witte, product manager, clinical software at Agilent, includes 180,000

probes divided into four samples. ìThis is the best balance of the num-

ber of samples and resolution,î she says. In addition, the Agilent Cy-

toGenomics 2.5 software compares the results from these arrays with

external and internal databases to distinguish between common varia-

tions and ones that could cause clinical problems.

Creating Custom Tools

To apply microarrays to clinical problems, physicians need approved

tools. One FDA-cleared diagnostic tool, the Pathwork Tissue of Origin

test from Pathwork Diagnostics in Redwood City, California, uses an

Affymetrix microarray to determine the tissue type in which a patientís

cancer started, such as breast or colon. Raji Pillai, senior director, prod-

uct development and clinical affairs at Pathwork Diagnostic says,

ìThis test uses formalin-fixed, paraffin-embedded [FFPE] tissue from a

patientís tumor and 2,000 transcript markers to provide a readout of a

tumorís gene-expression profile.î Using several thousand different tu-

mor specimens and proprietary computational algorithms, researchers

at Pathwork Diagnostics have identified a set of 2,000 genes that can be

used to distinguish 15 kinds of tumors.

When a pathologist receives a cancer sample that is difficult to iden-

tify visually, they can send it to Pathwork

Diagnostics. ìIt takes four to five days to

report out a result thatís interpreted by

a pathologist in our lab,î says David Cra-

ford, the companyís chief commercial

officer. A company pathologist reviews

the results to ensure the most accurate

interpretation of this diagnostic.

In the future, the company hopes to

develop microarray tests that determine

a tumorís tissue of origin and also dis-

tinguish between tumor subtypes. Such

advanced tests might even ìprovide in-

formation on the [patientís] predicted

response to a particular therapy,î Cra-

ford says.

In addition to being used for studying

an individualís genetic profile, microar-

rays can be used to explore genetic variations across different popula-

tions and cultures. For example, Jennifer Stone, market development

manager at Illumina in San Diego, California, says, ìWe developed our

Infinium HumanCore BeadChip family of microarrays to provide a so-

lution for population-level or biobank studies.î Such research involves

tens to hundreds of thousands of samples. ìThese genetic studies are

on a scale above and beyond whatís historically been done,î says Stone.

Because these microarrays accommodate a large number of samples,

they provide an opportunity for researchers to perform robust statisti-

cal analyses which can reveal differences in the distribution of genetic

variation between normal and diseased populations.

The HumanCore microarrays provide a standard set of over 300,000

SNP probes, which covers the entire genome and includes additional

probes specifically focused on ìvariants that exist in the population and

lead to the loss of function of genes,î explains Stone. These new micro-

arrays can also be customized, so researchers can study variants found

from their own experiments or from public databases.

To explore genetic variations across entire populations, researchers

need a family of flexible microarrays. Thus the second member of

the HumanCore family, the Infinium HumanCoreExome BeadChip,

includes the standard set of over 300,000 SNP probes plus 240,000

exome-focused markers. With this combination of markers, a scientist

can compare single nucleotide variations between samples and

potentially determine how they impact a proteinís production, as

indicated by the exome-based markers.

As companies begin to create increasingly customized CR

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Produced by the Science��������������������� ����� Genomics

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ìThe resolution

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860

tools, the concept of what makes a microarray has begun to evolve.

Traditionally, microarrays consisted only of nucleotides attached to

a solid surface, but variations on this theme also exist. For example,

Life Technologies (Carlsbad, California) developed its TaqMan

OpenArray Real-Time PCR plates, which include 3,072 wells.

ìThe arrays can be formatted from our inventory of eight million

TaqMan assays,î says Jami Elliott, market development manager

at Life Technologies. The real-time PCR assays, which use TaqMan

probes (so named because these assays rely on the Taq polymerase),

can be used to measure gene expression, identify biomarkers,

and more.

If eight million choices arenít enough, Joshua Trotta, director, busi-

ness development genetic analysis at Life Technologies, says, ìWe can

custom design one.î

Ongoing Data Dilemmas

Rather than making microarrays, Expression Analysis, a Quintiles

company in Durham, North Carolina, uses arrays to conduct a wide

range of studies for customers, such as gene-expression profiling. In

doing so, Expression Analysis uses microarrays from several vendors,

including Affymetrix, Illumina, and Fluidigm in South San Francisco,

California. According to Pat Hurban, vice president of R&D at

Expression Analysis, ìMicroarrays are very mature as a technology,

but there are still a number of challenges in working with the data,

especially when you want to drill down into the biology.î He adds,

ìItís one thing to provide a statistical treatment of data, but another to

understand the pathways involved and translate that into biology.î This

company uses a collection of proprietary tools in an effort to bridge that

knowledge gap.

In fact, Hurban advises researchers to reassess the best technology to

use as a project advances. ìYou must be mindful of the technical limita-

tions of microarrays,î he says. For example, he points out that micro-

arrays provide excellent discovery tools. ìItís not uncommon to iden-

tify specific genes of interest with microarrays,î Hurban says. ìWhen

it comes to translational research, the question becomes: Is it advisable

to continue on a microarray platform as you get closer to the clinic or

transition to a more suitable and robust technology, such as [quantita-

tive] PCR or sequencing.î

In a recent project, Expression Analysis worked with a client who had

what Hurban describes as ìa preliminary gene-signature panel that was

very useful as a diagnostic in a certain indication area.î Researchers at

Expression Analysis worked with patient samples from the sponsor to

put that signature on microarrays. ìWe showed the validity of this pan-

el,î Hurban says. ìUltimately, the sponsor wanted to turn this signature

into a diagnostic and became concerned with the microarray results

because the precision was a bit of a challenge.î Consequently, the client

eventually turned to a PCR-based platform for the final diagnostic. As

a result, Hurban says, ìYou might use a microarray to some point, and

then go to another technology.î

Tomorrowís Tools

The ongoing advances in sequencing technology have made more than a

few experts predict the demise of microarrays. For example, Elizabeth

Chao, director of translational medicine at Ambry Genetics in Aliso

Viejo, California, says, ìThe expression arrays that Iíve been using for

14 years are incredible tools, but RNA sequencing is starting to re-

place microarrays in research and translation.î She adds, ìSequencing

is not replacing microarrays in the clinical setting yet, but it probably

will soon.î

The data generated by sequencing can be both beneficial and challeng-

ing. Sequencing provides a gigantic amount of data in a short period of

time, but it can be difficult to interpret so much data. Chao is confident

that interpreting sequencing data will improve rapidly. She says, ìBioin-

formatics has really come up, and new methods are making it possible

to look at sequences across the entire genome.î

To evolve with changes in technology, some companies provide ser-

vices that teach researchers to use the growing amounts of data. For

example, Todd Smith, senior leader, research and application at Perki-

nElmer, says, ìWe can help people as they go from microarrays to

DNA sequencing.î This can include analytical techniques for handling

the higher volume of data. These technologies, though, will likely

complement each other, according to Smith and his colleagues. ìThere

are applications where microarrays work best, and others where se-

quencing works best,î says Williams. ìThere are areas where sequencing

wonít work well, but microarrays can.î As an example, Williams says

they are about to start a study that involves 160 samples that must be

processed in a matter of weeks. ìThereís no way we could go through

that with sequencing and get it turned around in time to have mean-

ingful data,î he says. Moreover, Smith says microarrays are superior

to sequencing when it comes to searching for structural variations in

a genome.

Though some experts may have differing opinions, the general con-

sensus predicts that microarrays will continue to benefit basic research

and provide clinical tools related to genomics. In the end, microarrays

will advance where they work the best.

Featured Participants

Affymetrixwww.affymetrix.com

Agilentwww.agilent.com

Ambry Genetics www.ambrygen.com

Expression Analysiswww.expressionanalysis.com

Illuminawww.illumina.com

Life Technologieswww.lifetechnologies.com

Oxford Gene Technologywww.ogt.co.uk

Pathwork Diagnosticswww.pathworkdx.com

PerkinElmerwww.perkinelmer.com

Washington University School of Medicine in St. Louis

medschool.wustl.edu

DOI: 10.1126/science.opms.p1300072

Mike May is a publishing consultant for science and technology.

Genomics

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13 - 17 F E B • C H I C A G O

2014

Meeting Global Challenges: Discovery and Innovation

Scientific discovery and innovation are helping to drive solutions to current and future global challenges.

Economic progress in every community worldwide has meanwhile become increasingly interdependent with

advances in science and technology. Challenges related to ensuring sufficient food for a growing population,

quality healthcare, renewable fuels, and a sustainable and enriching environment demand innovation and

international dialogue. Addressing these challenges depends upon discoveries emerging from the convergence

of physical, life, engineering, and social sciences in innovative ways that are most useful to society.

In a weakened global economy, many countries have begun to limit their investments in the future. Yet, invest-

ments in innovations – including funding for education as well as basic and applied research – represent our

best prospect for a sustainable environment and increased economic growth. Economists estimate, after all,

that innovation in science and technology are the source of more than half of the economic growth in many

countries. By increasing innovation in sustainable products and processes, world economies can continue to

enhance human welfare across society.

Innovation springs from the translation, production, and distribution of discovery and invention to society. In the

contemporary world, this is not a linear process, but rather, a matrix of interactions. Societies, with support from

public and private sectors and institutions, struggle to integrate the necessary disciplines and interests into this

matrix. Within the scientific and engineering community, we need to better integrate different disciplines and

voices into a consensus supporting innovation. Developed and developing countries that accomplish this will

become the economies of the future.

At the same time, it is imperative that we work in ways that are transparent and open to a diversity of contribu-

tors and ideas. Assessing risk versus benefit in adopting an innovation is complex and depends upon an open

dialogue. Only then will we realize the promise of furthering scientific discovery and innovation to meet pressing

global challenges and improve quality of life.

Call for Poster Submissions

Online entries will be accepted at www.aaas.org/meetings beginning 14 May 2013.

Symposium proposals for the 2014 AAAS Annual Meeting are now being solicited.

To submit a proposal, visit www.aaas.org/meetings. The deadline for submission is 23 April 2013.

Call for Symposium Proposals

PHOTO: ©CESAR RUSS PHOTOGRAPHY

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of pGL4 response element

vectors formapping

oncological pathways